Deformylase

Abstract

The invention provides def polypeptides and DNA (RNA) encoding def polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are methods for utilizing def polypeptides to screen for antibacterial compounds.

What is claimed is: 
     
       1. An isolated polynucleotide segment comprising: a first polynucleotide, sequence, or the full complement of the entire length of said first polynucleotide sequence, wherein the first polynucleotide sequence is (a) a reference sequence that encodes the amino acid sequence set forth in SEQ ID NO:2, or (b) is identical with the reference sequence except that, over the entire length corresponding to the reference sequence, the nucleic acid sequence has an average of up to thirty substitutions, deletions or insertions for every 100 nucleotides of the reference sequence. 
     
     
       2. The isolated polynucleotide segment of claim 1, comprising the first polynucleotide sequence wherein said first polynucleotide sequence is (a) identical with the reference sequence, or (b) identical with the reference sequence except that, over the entire length corresponding to the reference sequence, the nucleic acid sequence has an average of up to five substitutions, deletions or insertions for every 100 nucleotides of the reference sequence. 
     
     
       3. The isolated polynucleotide segment of claim 2, wherein said first polynucleotide sequence encodes a deformylase polypeptide. 
     
     
       4. The isolated polynucleotide segment of claim 1, wherein said isolated polynucleotide comprises the full complement sequence, which is the complement of said first polynucleotide sequence wherein said first polynucleotide sequence which is (a) identical with the reference sequence, or (b) identical with the reference sequence except that, over the entire length corresponding to the reference sequence, the nucleic acid sequence has an average of up to five substitutions, deletions or insertions for every 100 nucleotides of the reference sequence. 
     
     
       5. The isolated polynucleotide segment of claim 4, wherein said first polynucleotide sequence encodes a deformylase polypeptide. 
     
     
       6. A vector comprising the polynucleotide segment of claim 1. 
     
     
       7. An isolated host cell transfected with the vector of claim 6. 
     
     
       8. A process for producing a deformylase polypeptide of the first polynucleotide sequence comprising the step of culturing the host of claim 7 under conditions sufficient for the production of said polypeptide. 
     
     
       9. An isolated polynucleotide segment of claim 1, wherein said first polynucleotide sequence is (a) identical with the reference sequence, or (b) is identical with the reference sequence except that, over the entire length corresponding to the reference sequence, the nucleic acid sequence has an average of up to ten substitutions, deletions or insertions for every 100 nucleotides of the reference sequence. 
     
     
       10. The isolated polynucleotide segment of claim 1, wherein: (1) the first polynucleotide sequence is (a) a second reference sequence which encodes the same mature polypeptide, expressed by the polypeptide deformylase gene contained in Chlamydia trachomatis, or (b) is identical with the second reference sequence except that, over the entire length corresponding to the second reference sequence, the nucleic acid sequence has an average of up to thirty substitutions, deletions or insertions for every 100 nucleotides of the second reference sequence, or   (2) the full complement of the entire length of said first polynucleotide sequence.   
     
     
       11. An isolated polynucleotide segment of claim 10, wherein said first polynucleotide sequence is (a) identical with the second reference sequence, or (b) is identical with the second reference sequence except that, over the entire length corresponding to the second reference sequence, the nucleic acid sequence has an average of up to five substitutions, deletions or insertions for every 100 nucleotides of the second reference sequence. 
     
     
       12. An isolated polynucleotide segment of claim 10 comprising a first polynucleotide sequence encoding the same mature polypeptide expressed by the polypeptide deformylase gene contained in Chlamydia trachomatis, or the full complement of the entire length of said first polynucleotide sequence. 
     
     
       13. A recombinant polynucleotide segment comprising nucleotides 1 to 543 of the polynucleotide sequence set forth in SEQ ID NO: 1, or the full complement of the entire length of nucleotides 1 to 543 of the polynucleotide sequence set forth in SEQ ID NO: 1. 
     
     
       14. A recombinant polynucleotide segment which encodes a polypeptide comprising a region having the amino acid sequence of SEQ ID NO:2, or the full complement of the entire length of the encoding polynucleotide sequence. 
     
     
       15. A vector comprising the recombinant polynucleotide of claim 14. 
     
     
       16. An isolated host cell transfected with the vector of claim 15. 
     
     
       17. A process for producing a deformylase polypeptide of the encoding polynucleotide sequence comprising the step of culturing the host cell of claim 16 under conditions sufficient for the production of said polypeptide. 
     
     
       18. An isolated polynucleotide segment, comprising: a first polynucleotide sequence, wherein said first polynucleotide sequence hybridizes to the full complement of a reference polynucleotide sequence, wherein said reference polynucleotide sequence is (a) the polynucleotide sequence set forth in SEQ ID NO: 1, or (b) identical with the polynucleotide sequence set forth in SEQ ID NO: 1 except that, over the entire length corresponding to the polynucleotide sequence set forth in SEQ ID NO: 1, the reference polynucleotide sequence has an average of up to five substitutions, deletions or insertions for every 100 nucleotides of the polynucleotide sequence set forth in SEQ ID NO: 1; and wherein the hybridization conditions include incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 micrograms/ml denatured, sheared salmon sperm DNA, followed by washing in 0.1 ×SSC at about 65° C. 
     
     
       19. The polynucleotide of claim 1, 9, 10, 11 or 18, wherein said polynucleotide encodes a deformylase polypeptide. 
     
     
       20. The isolated polynucleotide segment of claim 18, wherein said reference polynucleotide sequence is (a) identical with the polynucleotide sequence set forth in SEQ ID NO: 1 or (b) identical with the polynucleotide sequence set forth in SEQ ID NO: 1 except that, over the entire length corresponding to the polynucleotide sequence set forth in SEQ ID NO: 1, the reference polynucleotide sequence has an average of up to three substitutions, deletions or insertions for every 100 nucleotides of the polynucleotide sequence set forth in SEQ ID NO: 1. 
     
     
       21. The isolated polynucleotide segment of claim 18, wherein said first polynucleotide sequence hybridizes to the full complement of the polynucleotide sequence of SEQ ID NO: 1, wherein hybridization conditions include incubation at 42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardt's solution, 10% dextran sulfate, and 20 micrograms/ml denatured, sheared salmon sperm DNA, followed by washing in 0.1×SSC at about 65° C. 
     
     
       22. A composition comprising the isolated polynucleotide of claim 1, which polynucleotide is according to the formula:   X--(R.sub.1).sub.n --(PN)--(R.sub.2).sub.n --Y     wherein, at the 5' end of the molecule, X is hydrogen, and at the 3' end of the molecule, Y is hydrogen or a metal, each occurrence of R 1  and R 2  is independently any nucleic acid residue or, n is an integer between 1 and 1000, and PN is the isolated polynucleotide of claim 1.